Moeed wrote:
Thank you Justin for your reply. Simulation is 5 ns long ( before this a
500 ps NVT was done as equilibration) and total energy has been
equilibrated after around 3 ns.
-b is set to 4000 that is the last 1 ns has been used for rdf.
For all but the simplest systems this simulation length and data analysis period
is insufficient. How big is your polymer? Proper sampling may take tens to
hundreds of ns of data collection.
-Justin
Best,
moeed
On Fri, Sep 9, 2011 at 3:37 PM, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Moeed wrote:
Dear users,
I have created radial distribution function plot for Carbon
atoms in a system containing polymer chains. I see some little
jumps between first and second peak.
I need your help to comment on how this behavior can be
justified (or if the plot is wrong).
g_rdf -f *.trr -s *.tpr -o *.xvg -n *.ndx –b xxx
How long is the sampling? In the absence of -e and with -b being
hidden from us for some unknown reason, it's hard to guess. I'd say
your simulation just isn't fully converged, although for complex
systems that can be a challenge anyway. Nothing unusual.
-Justin
--
==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
<tel:%28540%29%20231-9080>
http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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